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GC GC vitamin D binding protein [ Homo sapiens (human) ]

Gene ID: 2638, updated on 3-Nov-2024

Summary

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Official Symbol
GCprovided by HGNC
Official Full Name
GC vitamin D binding proteinprovided by HGNC
Primary source
HGNC:HGNC:4187
See related
Ensembl:ENSG00000145321 MIM:139200; AllianceGenome:HGNC:4187
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DBP; VDB; GRD3; VDBG; VDBP; GcMAF; DBP/GC; Gc-MAF; DBP-maf; HEL-S-51
Summary
The protein encoded by this gene belongs to the albumin gene family. It is a multifunctional protein found in plasma, ascitic fluid, cerebrospinal fluid and on the surface of many cell types. It binds to vitamin D and its plasma metabolites and transports them to target tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]
Expression
Restricted expression toward liver (RPKM 1264.0) See more
Orthologs
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Genomic context

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Location:
4q13.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (71741693..71805520, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (75084117..75147957, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (72607410..72671237, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:72458772-72459481 Neighboring gene uncharacterized LOC107986285 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:72479894-72481093 Neighboring gene uncharacterized LOC105377271 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:72519382-72520581 Neighboring gene RNA, 5S ribosomal pseudogene 163 Neighboring gene VISTA enhancer hs2570 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:72836369-72836534 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:72897326-72897928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:72960191-72960690 Neighboring gene neuropeptide FF receptor 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:72977919-72979118 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:73019056-73019842 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 3 Neighboring gene Sharpr-MPRA regulatory region 5509

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Vitamin D-binding protein as a biomarker of active disease in acute intermittent porphyria. Serrano-Mendioroz I, et al. J Proteomics, 2015 Sep 8. PMID 25979770
  2. Genetic polymorphisms of the vitamin D binding protein and plasma concentrations of 25-hydroxyvitamin D in premenopausal women. Sinotte M, et al. Am J Clin Nutr, 2009 Feb. PMID 19116321
  3. Effects of vitamin D binding protein phenotypes and vitamin D supplementation on serum total 25(OH)D and directly measured free 25(OH)D. Sollid ST, et al. Eur J Endocrinol, 2016 Apr. PMID 26733479, Free PMC Article
  4. Characterization of mutants of the vitamin D-binding protein/group-specific component: molecular evolution of GC*1A2 and GC*1A3, common in some Asian populations. Yuasa I, et al. Hum Genet, 1995 May. PMID 7759070
  5. Genetic variants in the vitamin D pathway genes VDBP and RXRA modulate cutaneous melanoma disease-specific survival. Yin J, et al. Pigment Cell Melanoma Res, 2016 Mar. PMID 26575331, Free PMC Article

See all (398) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease.
    Title: Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease.
  2. Association of rs4588 polymorphism in vitamin D binding protein gene with polycystic ovarian syndrome in Iranian women: a case-control study.
    Title: Association of rs4588 polymorphism in vitamin D binding protein gene with polycystic ovarian syndrome in Iranian women: a case-control study.
  3. Relationship between Vitamin D3 Deficiency, Metabolic Syndrome and VDR, GC, and CYP2R1 Gene Polymorphisms.
    Title: Relationship between Vitamin D3 Deficiency, Metabolic Syndrome and VDR, GC, and CYP2R1 Gene Polymorphisms.
  4. Association between the genetic variant in the vitamin D pathway (rs2282679), circulating 25-hydroxyvitamin D levels, insulin resistance and metabolic syndrome criteria.
    Title: Association between the genetic variant in the vitamin D pathway (rs2282679), circulating 25-hydroxyvitamin D levels, insulin resistance and metabolic syndrome criteria.
  5. Vitamin D receptor and binding protein genes variants in patients with migraine.
    Title: Vitamin D receptor and binding protein genes variants in patients with migraine.
  6. Vitamin D-Binding Protein and the Role of its Gene Polymorphisms in the Mortality of Sepsis Patients.
    Title: Vitamin D-Binding Protein and the Role of its Gene Polymorphisms in the Mortality of Sepsis Patients.
  7. Genetic influence on urinary vitamin D binding protein excretion and serum levels: a focus on rs4588 C>A polymorphism in the GC gene.
    Title: Genetic influence on urinary vitamin D binding protein excretion and serum levels: a focus on rs4588 C>A polymorphism in the GC gene.
  8. Vitamin D receptor rs3782905 and vitamin D binding protein rs7041 polymorphisms are associated with hepatocellular carcinoma susceptibility in cirrhotic HCV patients.
    Title: Vitamin D receptor rs3782905 and vitamin D binding protein rs7041 polymorphisms are associated with hepatocellular carcinoma susceptibility in cirrhotic HCV patients.
  9. The Molecular Aspects of Functional Activity of Macrophage-Activating Factor GcMAF.
    Title: The Molecular Aspects of Functional Activity of Macrophage-Activating Factor GcMAF.
  10. Sex-Specific Variations in Vitamin D and Vitamin D Binding Protein (Vdbp) and Flipped Pattern of their Association in Preeclamptic Women with Dyslipidemia.
    Title: Sex-Specific Variations in Vitamin D and Vitamin D Binding Protein (Vdbp) and Flipped Pattern of their Association in Preeclamptic Women with Dyslipidemia.
Submit: New GeneRIF Correction See all GeneRIFs (310)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Association between liver-specific gene polymorphisms and their expression levels with nonalcoholic fatty liver disease.
EBI GWAS Catalog
Common genetic determinants of vitamin D insufficiency: a genome-wide association study.
EBI GWAS Catalog
Genome-wide association analysis of circulating vitamin D levels in children with asthma.
EBI GWAS Catalog
Genome-wide association study of circulating vitamin D levels.
EBI GWAS Catalog
Genome-wide association study of circulating vitamin D-binding protein.
EBI GWAS Catalog
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
EBI GWAS Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables calcidiol binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables vitamin D binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables vitamin transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in vitamin D metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vitamin D metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in vitamin transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in vitamin transport TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in blood microparticle HDA PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular region NAS
Non-traceable Author Statement
more info
 PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in extracellular space HDA PubMed 
located_in lysosomal lumen TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
vitamin D-binding protein
Names
epididymis secretory protein Li 51
gc protein-derived macrophage activating factor
gc-globulin
group-specific component (vitamin D binding protein)
vitamin D-binding alpha-globulin
vitamin D-binding protein-macrophage activating factor
NP_000574.2
NP_001191235.1
NP_001191236.1
XP_006714240.1
XP_054205648.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012837.3 RefSeqGene

    Range
    26442..68824
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000583.4 → NP_000574.2  vitamin D-binding protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_000574.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is a predominant transcript. This variant and variant 2 encode the same isoform (1).
    Source sequence(s)
    AA702473, AK223458, X03178
    Consensus CDS
    CCDS3550.1
    UniProtKB/Swiss-Prot
    B4DPP2, D6RAK8, P02774, Q16309, Q16310, Q53F31, Q6GTG1
    UniProtKB/TrEMBL
    V9HWI6
    Related
    ENSP00000273951.8, ENST00000273951.13
    Conserved Domains (2) summary
    smart00103
    Location:19 → 201
    ALBUMIN; serum albumin
    pfam09164
    Location:405 → 469
    VitD-bind_III; Vitamin D binding protein, domain III

  2. NM_001204306.1 → NP_001191235.1  vitamin D-binding protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_001191235.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR and encodes the same isoform 1, as compared to variant 1.
    Source sequence(s)
    AA702473, AK223458
    Consensus CDS
    CCDS3550.1
    UniProtKB/Swiss-Prot
    B4DPP2, D6RAK8, P02774, Q16309, Q16310, Q53F31, Q6GTG1
    UniProtKB/TrEMBL
    V9HWI6
    Conserved Domains (2) summary
    smart00103
    Location:19 → 201
    ALBUMIN; serum albumin
    pfam09164
    Location:405 → 469
    VitD-bind_III; Vitamin D binding protein, domain III

  3. NM_001204307.1 → NP_001191236.1  vitamin D-binding protein isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 5' sequence which contains an upstream in-frame AUG start codon, as compared to variant 1. The resulting isoform (2) has a longer N-terminus, as compared to isoform 1.
    Source sequence(s)
    AA702473, AC024722, AK223458, AK309595, AK315853
    Consensus CDS
    CCDS56332.1
    UniProtKB/TrEMBL
    V9HWI6
    Related
    ENSP00000421725.1, ENST00000504199.5
    Conserved Domains (2) summary
    smart00103
    Location:38 → 220
    ALBUMIN; serum albumin
    pfam09164
    Location:424 → 488
    VitD-bind_III; Vitamin D binding protein, domain III

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    71741693..71805520 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714177.3 → XP_006714240.1  vitamin D-binding protein isoform X1

    UniProtKB/TrEMBL
    V9HWI6
    Related
    ENSP00000422664.1, ENST00000509740.5
    Conserved Domains (1) summary
    smart00103
    Location:19 → 201
    ALBUMIN; serum albumin

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    75084117..75147957 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349673.1 → XP_054205648.1  vitamin D-binding protein isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P02774.2 GenPept UniProtKB/Swiss-Prot:P02774

Gene LinkOut

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